For several years, animal welfare concerns have been raised over the practice of shooting Greyheaded Flying-foxes (GHFF) in commercial fruit orchards in Australia, and the role of government agencies in licensing the kill. In NSW the practice is poorly monitored and insufficient evidence has been available to assess welfare concerns. This study reports the first systematically acquired data on flying-foxes shot under licence in NSW. In the 2006/07 season the average number of GHFFs licensedto be harmed was <40 individuals per licence. Despite this, a total of 164 dead or injured flying-foxeswere collected (n = 146) or observed (n = 18) from an orchard in western Sydney over two weeks inspring 2007, after shooting had occurred at the orchard to protect fruit crops. Detailed information,including sex, reproductive state, age and description of injuries, was compiled on 136 collected bats. The sex ratio was strongly skewed towards females (1:1·73), of which 54 (65%) were lactating at the time. Thirteen of these were shot while carrying their dependent young, while 41 neonates would have been left behind in the camp to die. Hence, the total estimate of flying-foxes that died due to shooting in the orchard over the two-week period was 205. Collected bats suffered from various injuries, and at least 30% (44% including the neonates left in the camp) were alive and unattended more than 8.5 hours after shooting. This is in contravention of the definition of ‘humane killing’ and the Prevention of Cruelty to Animals Act 1979. Importantly, the GHFF is vulnerable under NSW and Federal legislations and the killing of reproducing females in crops contributes to its declining numbers, making Sydney Basin an ecological trap for this species.